As its previous version, we should have more Alchemical Things.
Pahimar added some kind of machines - the Aludel and the Calcinator. I have some ideas for them:

Aludel = It wont open any GUI unless you put a Glass Bell on it; when you fuel it, steam particles start flowing; its use could be to mix things and make another item (exemple: 4x Ash/Coal Dust = 1x Alchemical Coal); also, I'd make its texture 16x16.

Calcinator = Turns liquid things (created on a new machine :D) into dusts from the mod. Pahimar should make the liquid appear, and fire particles appear on the bottom. Also, I'd make its texture 16x16.

Crusher = Turns ores/items into liquid forms of them, which will be used on the Calcinator for making dusts.

Matter Morpher = Used to Morph items and put EMC inside them to make another item.

Dusts:
Ash = Coal
Minium Dust = Shard of Minium
Verdant Dust = Emerald
Azure Dust = Diamond
Amaranthine Dust = Azure Dust + 4 Gold Ingots on the Aludel
Iridescent Dust = 2 Mobius Fuel + Amaranthine Dust

As Pahimar doesn't want Red Matter, Dark Matter would be crafted like so:
Mix Coal in the Aludel until you get the Aeternalis Fuel. Then, crush them on the Crusher to make its liquid. After that, pipe or use buckets to put this liquid on the Calcinator. You'll need 8000mb of this liquified Aeternalis Fuel. After that, it'll make one Aeternalis Compound. Use this item to mix with 8 Obsidian on the Aludel. After that, you'll have a Primitive Matter. Put this item with an Inert Stone to get the next stage: Physical Matter. Finally, put the Physical Matter with a Block of Diamond and an EMC Value of 8192 into the Matter Morpher to make a Dark Matter.

EMC Piping and Machines Power

As Pahimar wanted, there should be EMC Pipes. I was thinking of the following:
16 of them could be made by 1 block of iron surrounded by 4 Alchemical Coal and some glass, like the crafting above:

B = Block of Iron
A = Alchemical Coal
G = Glass

GAG
ABA
GAG

But, if you want to transfer EMC, you would need an Energy Condenser in order to condense items into EMC.

You can also power the machines with EMC if you don't want to lose solid fuel, such as Coal or Wood.

Difference between the Minium Stone and the Philosopher's Stone

The Minium Stone has uses, and the Philosopher doesn't. The Philosopher's Stone also has its own Crafting Grid. Also, the Philosopher's Stone can transmutate blocks on the ground.

Crafting:
Minium Stone = current
Philosopher's Stone = Mixing a fully charged Minium Stone with 4 Azure Dusts on the Aludel would make a Mixed Stone. Throw it on the Matter Morpher with 4 Redstone Dust and 4 Glowstone Dust and with 256 EMC to make the Philosopher's Compound. Throw it on some Red Water to make the Philosopher's Stone.

Alchemical Chest: Pahimar should fix the Alchemical Chest's texture, which has a little problem around the locker.

I would also make some magic items with the Aludel and the Matter Morpher, such as those EE2 rings and some Staffs, but that's Pahimar's choice :)

I hope you liked my ideas :D

-Gathe3

Seems cool, I hope Pahimar reads this!

Thanks!

There are a few things I'd like to point out

• Pahimar does not want to add world gen to EE3, so Amethyst and Tungsten are kinda out the door.
• While the process of creating Dark Matter seems interesting, it feels a bit too cheap and too easy to make. A few more steps and more (expensive) materials would make it a bit more balanced (instead of mixed coal, have Obsidian, require more than 8 buckets of liquid Aeternalis Fuel, maybe involve Minium Shards, etc)
• The Minium to Philosopher's stone upgrade still seems a bit cheap to me, though I can't think off the top of my head what would be a good replacement recipe.

Other wise, pretty neat ideas.

pahimar has stated before that you'll need red water to create the Philosopher's Stone in-world (ie multi-block structures). At least I'm pretty sure he said that.

I wrote these ideas almost based on the EE2. When I did that, I forgot that this mod was way OP. Thank you all for the things :)

I've updated some things on the post, please check that out :)

There's already a purpose for the calcinator. It turns stuff with EMC value into dust. Emeralds give you Minium Dust, and cobble gives you ash.

Nice ideas, but plans already in motion :)